Not going to put words in the GP's mouth, but my take is because:
(a) Cheer up, emo kid.
(b) You presuppose that all base instincts are bad (e.g. you reference them as "crap"). It's kind of Victorian.
(c) What base instinct produced your first post? Did you feel that if you posted a view that was anti-humanity that you would distinguish yourself from the herd and get you noticed by potential mates? On /.?
(d) Your argument is reductionist and nihilistic (see (a)): "If people tend to do bad things, society will tend to do bad things. If civilizations have done bad things, they will always tend to do bad things." The problem with reductionism is that it's possible to argue that any altruistic action is done purely to enhance ones own esteem. It's possible that no form of art has ever had merit, and that the advancement of science and knowledge serve only to further the dominance of alpha males. But it's also possible to argue the converse for evil actions. You could argue that there's no reason not to 'cull the herd' of weaklings, as they will taint the gene pool. I disagree with you for the same reason that I disagree with Ayn Rand. There's no room for nuance.
(e) An alternate possibility to "Society and civilization are simply entities that over time evolved on top of all this crap" is that society and civilization function as ways to prevent us from purely acting on base instincts, and that we've actually learned some lessons from history. We stumble along, and different peoples' base drives will direct them to push for a different society, but we have evolved societal rules that have actually protected us from too many crimes in any particular direction. There are certainly conflicts and crimes between family members, between neighbors, between states, between countries, and certainly the winners are usually the 'stronger'. I just think the failings are instances where our societal rules still have room for improvement, not as an indictment against our species ever being any better. It's only been a relatively short period of time since humans were able to talk to anyone on the planet in real-time.
Just my two cents,
-t.